Notes
- Unclassified reads were excluded
- Taxa with total reads number of 10 or lower were excluded
- Eukaryotes were excluded from the analyis
Import Exp data
MCM D6300
MCM D6331
FR D6323
Canis lupus
Homo sapiens
Merge
Filter Exp data
Filter samples based on total read count
Fix sample names
Gold Standard Data
Exclude (truly) unclassified reads
Convert NA to ‘missing’ in the taxonomy table (to
avoid errors)
Number of NAs fo each rank level:
## superkingdom phylum class order family genus
## 0 0 0 0 0 0
## species Gram.Stain
## 0 7
‘missing’ means that there is no associated taxon level for
the given taxon, but the read itself was classified.
This should be considered when glomerating taxa, as ‘missing’
taxa can be derived from different lineages.
To avoid this, the glomerating should be done using:
ignore_lineage=F
Filter for taxa below threshold
Taxon IDs
## using species as taxon identifier
Fix genera
## Glomerating all hits from: Veillonella to: Veillonella rogosae
## Glomerating all hits from: Faecalibacterium to: Faecalibacterium prausnitzii
## Glomerating all hits from: Prevotella to: Prevotella corporis
## Glomerating all hits from: Roseburia to: Roseburia hominis
Fix species
## Glomerating all hits from: Bacteroides fragilis to: Bacteroides fragilis
## Glomerating all hits from: Bacteroides fragilis CAG:47 to: Bacteroides fragilis
## Glomerating all hits from: Bacteroides fragilis_A to: Bacteroides fragilis
Fix sample names from ‘-’
Merge exp data with GS
Filter Taxa for Gold Standard
These are the taxa that were found in the experimental data
| Bacillus subtilis |
1423 |
Bacteria |
Firmicutes |
Bacilli |
Bacillales |
Bacillaceae |
Bacillus |
1740000 |
+ |
2822873.2 |
| Enterococcus faecalis |
1351 |
Bacteria |
Firmicutes |
Bacilli |
Lactobacillales |
Enterococcaceae |
Enterococcus |
990000 |
+ |
1451302.3 |
| Escherichia coli |
562 |
Bacteria |
Proteobacteria |
Gammaproteobacteria |
Enterobacterales |
Enterobacteriaceae |
Escherichia |
1010000 |
- |
1450435.4 |
| Limosilactobacillus fermentum |
1613 |
Bacteria |
Firmicutes |
Bacilli |
Lactobacillales |
Lactobacillaceae |
Limosilactobacillus |
1840000 |
+ |
2345749.4 |
| Listeria monocytogenes |
1639 |
Bacteria |
Firmicutes |
Bacilli |
Bacillales |
Listeriaceae |
Listeria |
1410000 |
+ |
1850634.6 |
| Pseudomonas aeruginosa |
287 |
Bacteria |
Proteobacteria |
Gammaproteobacteria |
Pseudomonadales |
Pseudomonadaceae |
Pseudomonas |
420000 |
- |
445095.9 |
| Salmonella enterica |
28901 |
Bacteria |
Proteobacteria |
Gammaproteobacteria |
Enterobacterales |
Enterobacteriaceae |
Salmonella |
1040000 |
- |
1210133.4 |
| Staphylococcus aureus |
1280 |
Bacteria |
Firmicutes |
Bacilli |
Bacillales |
Staphylococcaceae |
Staphylococcus |
1550000 |
+ |
2060483.9 |
Add Gram Stain Info
Omit Eukaryotes
Relative abundance of taxa at each taxonomic level
Parameters and Settings
Correlation
PERMANOVA model
Gram Stain level
Barplot of abundances

Phylum level
Barplot of abundacnes

MAASLIN2 - Number of Significantly Different Taxa Among FR,
H. sapiens and C. lupus

Barplot of Coefficients

Heatmap of Significant Associations (−log(qval) x
sign(coeff))

PERMANOVA
| primer |
2 |
0.2220239 |
0.1815434 |
2.661743 |
0.069 |
| Residual |
24 |
1.0009559 |
0.8184566 |
NA |
NA |
| Total |
26 |
1.2229798 |
1.0000000 |
NA |
NA |

Class level
Barplot of abundances

MAASLIN2 - Number of Significantly Different Taxa Among FR,
H. sapiens and C. lupus

Barplot of Coefficients

Heatmap of Significant Associations (−log(qval) x
sign(coeff))

PERMANOVA
| primer |
2 |
0.2551431 |
0.1460105 |
2.051694 |
0.047 |
| Residual |
24 |
1.4922872 |
0.8539895 |
NA |
NA |
| Total |
26 |
1.7474303 |
1.0000000 |
NA |
NA |

Order level
Barplot of abundances

MAASLIN2 - Number of Significantly Different Taxa Among FR,
H. sapiens and C. lupus

Barplot of Coefficients

Heatmap of Significant Associations (−log(qval) x
sign(coeff))
### PERMANOVA
| primer |
2 |
0.2509976 |
0.1403119 |
1.958551 |
0.056 |
| Residual |
24 |
1.5378566 |
0.8596881 |
NA |
NA |
| Total |
26 |
1.7888542 |
1.0000000 |
NA |
NA |

Family level
Barplot of abundances

MAASLIN2 - Number of Significantly Different Taxa Among FR,
H. sapiens and C. lupus

Barplot of Coefficients

Heatmap of Significant Associations (−log(qval) x
sign(coeff))

PERMANOVA
| primer |
2 |
0.3283757 |
0.1074244 |
1.444239 |
0.005 |
| Residual |
24 |
2.7284326 |
0.8925756 |
NA |
NA |
| Total |
26 |
3.0568083 |
1.0000000 |
NA |
NA |

Genus level
Barplot of abundances

MAASLIN2 - Number of Significantly Different Taxa Among FR,
H. sapiens and C. lupus

Barplot of Coefficients

Heatmap of Significant Associations (−log(qval) x
sign(coeff))

PERMANOVA
| primer |
2 |
0.2487811 |
0.0619096 |
0.7919443 |
0.014 |
| Residual |
24 |
3.7696752 |
0.9380904 |
NA |
NA |
| Total |
26 |
4.0184563 |
1.0000000 |
NA |
NA |

Species level
Barplot of abundances

MAASLIN2 - Number of Significantly Different Taxa Among FR,
H. sapiens and C. lupus

Barplot of Coefficients
